title: Optimizing the kinetics and thermodynamics of DNA i-motif folding.
abstract: Under slightly acidic conditions, single cytidine-rich DNA strands can form four-stranded structures called i-motifs. The stability of the i-motif structure is based on the intercalation of hemiprotonated C-C(+) base pairs. In addition, the stability of these structures is influenced by pH, temperature, salt concentration, number of cytidines per C-rich stretch, and length of sequence; it also depends on the nucleotides in the connecting loop regions. Here, we investigated the influence of the loop nucleotides on i-motif stability, structure, and kinetics of folding, in five structures with the same loop-size but different adenosine and thymidine residues within the loop. The stabilities of the i-motif structures were determined by CD melting, and structure and kinetics of folding were studied by static and time-resolved NMR experiments.
authors.affiliation: Institute for Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Straße 7, 60438 Frankfurt Germany.
authors.forename: Anna Lena
authors.initials: AL
authors.lastname: Lieblein
authors.forename: Boris
authors.initials: B
authors.lastname: Fürtig
authors.forename: Harald
authors.initials: H
authors.lastname: Schwalbe
mesh_terms: D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D059372:Nucleotide Motifs; D056951:Photoelectron Spectroscopy; D013816:Thermodynamics
chemical_list: D004247:DNA
keywords: DNA dynamics; DNA structures; i-motif; quadruplex structures; time-resolved spectroscopy